A protocol is a set of procedure or system of activities that define how something operates. The difference between a protocol and an algorithm is that protocols are typically standardized for their functions. The most popular example being TCP/IP (Internet Protocol). TCP is a transmission control protocol that is used by ALL applications built using the internet. However alternatives do exist, they are non standardized and thus incur added security risks.
Protocols exist across ever dimension of technology, from communications, to privacy preservation, to value transfer, to digital renderings, and beyond.